Package: beadplexr 0.5.0.999
beadplexr: Analysis of Multiplex Cytometric Bead Assays
Reproducible and automated analysis of multiplex bead assays such as CBA (Morgan et al. 2004; <doi:10.1016/j.clim.2003.11.017>), LEGENDplex (Yu et al. 2015; <doi:10.1084/jem.20142318>), and MACSPlex (Miltenyi Biotec 2014; Application note: Data acquisition and analysis without the MACSQuant analyzer; <https://www.miltenyibiotec.com/upload/assets/IM0021608.PDF>). The package provides functions for streamlined reading of fcs files, and identification of bead clusters and analyte expression. The package eases the calculation of standard curves and the subsequent calculation of the analyte concentration.
Authors:
beadplexr_0.5.0.999.tar.gz
beadplexr_0.5.0.999.zip(r-4.5)beadplexr_0.5.0.999.zip(r-4.4)beadplexr_0.5.0.999.zip(r-4.3)
beadplexr_0.5.0.999.tgz(r-4.4-any)beadplexr_0.5.0.999.tgz(r-4.3-any)
beadplexr_0.5.0.999.tar.gz(r-4.5-noble)beadplexr_0.5.0.999.tar.gz(r-4.4-noble)
beadplexr_0.5.0.999.tgz(r-4.4-emscripten)beadplexr_0.5.0.999.tgz(r-4.3-emscripten)
beadplexr.pdf |beadplexr.html✨
beadplexr/json (API)
NEWS
| # Install 'beadplexr' in R: |
| install.packages('beadplexr', repos = c('https://ustervbo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://gitlab.com/ustervbo/beadplexr
Last updated 1 years agofrom:887b760902. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 11 2024 |
| R-4.5-win | OK | Sep 11 2024 |
| R-4.5-linux | OK | Sep 11 2024 |
| R-4.4-win | OK | Sep 11 2024 |
| R-4.4-mac | OK | Sep 11 2024 |
| R-4.3-win | OK | Sep 11 2024 |
| R-4.3-mac | OK | Sep 11 2024 |
Exports:approx_adjustas_data_frame_analytebp_clarabp_dbscanbp_density_cutbp_kmeansbp_mclustcalc_analyte_mficalc_std_conccalculate_concentrationdensity_cutdespeckledist_chebyshevdo_find_turning_pointsfacs_density1dfacs_density2dfacs_hexbinfacs_plotfacs_scatterfit_standard_curveidentify_analyteidentify_cba_analyteidentify_legendplex_analyteidentify_macsplex_analyteload_panelplot_estimateplot_std_curveplot_target_est_concread_fcstrim_populationturning_point
Dependencies:abindbackportsbootbroomcarcarDataclasscliclustercodetoolscolorspacecowplotcpp11DEoptimRDerivdiptestdoBydplyrdrcfansifarverflexmixfpcgenericsggplot2gluegtablegtoolsisobandkernlablabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmclustmgcvmicrobenchmarkminqamodelrmodeltoolsmultcompmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplotrixprabcluspurrrquantregR6RColorBrewerRcppRcppEigenrlangrobustbasesandwichscalesSparseMstringistringrsurvivalTH.datatibbletidyrtidyselectutf8vctrsviridisLitewithryamlzoo
Analysis of LEGENDplex data with beadplexr
Rendered fromlegendplex_analysis.Rmdusingknitr::rmarkdownon Sep 11 2024.Last update: 2023-06-13
Started: 2020-04-04
beadplexr with CBA and MACSPlex assays
Rendered fromcba_macsplex_example.Rmdusingknitr::rmarkdownon Sep 11 2024.Last update: 2023-06-13
Started: 2018-03-06
Preparing flow-data for use with with beadplexr
Rendered frompreparing_flow_data.Rmdusingknitr::rmarkdownon Sep 11 2024.Last update: 2023-06-13
Started: 2020-04-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Approximate bandwidth adjustment. | approx_adjust |
| Cast list of analytes to 'data.frame' | as_data_frame_analyte |
| Calculate the analyte intensity | calc_analyte_mfi |
| Calculate standard concentration | calc_std_conc |
| Calculate concentration. | calculate_concentration |
| Clustering with trimming | bp_clara bp_dbscan bp_density_cut bp_kmeans bp_mclust cluster_events |
| Despeckle parameters | despeckle |
| Chebyshev distance | dist_chebyshev |
| Plot FACS data. | facs_density1d facs_density2d facs_hexbin facs_plot facs_scatter |
| Fit a standard curve | fit_standard_curve |
| Identify analyte | identify_analyte |
| Identify multiplex assay analytes | identify_assay_analyte identify_cba_analyte identify_legendplex_analyte identify_macsplex_analyte |
| Load panel information | load_panel |
| LEGENDplex example data | lplex |
| Plot concentrations | plot_concentrations plot_estimate plot_std_curve plot_target_est_conc |
| Read a fcs file. | read_fcs |
| Simulated beadplex data | simplex |
| Trim cluster. | trim_population |
| Turning points | turning_point |
